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- PDB-1puq: Solution Structure of the MutT Pyrophosphohydrolase Complexed wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1puq | ||||||
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Title | Solution Structure of the MutT Pyrophosphohydrolase Complexed with Mg(2+) and 8-oxo-dGMP, a Tightly-bound Product | ||||||
![]() | Mutator mutT protein | ||||||
![]() | HYDROLASE / MUTATOR PROTEIN / NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE / MUTT PYROPHOSPHOHYDROLASE-METAL-PRODUCT COMPLEX | ||||||
Function / homology | ![]() dGDP catabolic process / 8-oxo-dGTP diphosphatase / 8-oxo-GDP phosphatase activity / 8-oxo-dGDP phosphatase activity / dGTP catabolic process / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / nucleotide-excision repair / manganese ion binding / DNA replication ...dGDP catabolic process / 8-oxo-dGTP diphosphatase / 8-oxo-GDP phosphatase activity / 8-oxo-dGDP phosphatase activity / dGTP catabolic process / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / nucleotide-excision repair / manganese ion binding / DNA replication / DNA repair / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / simulated annealing torsion angle dynamics | ||||||
![]() | Massiah, M.A. / Saraswat, V. / Azurmendi, H.F. / Mildvan, A.S. | ||||||
![]() | ![]() Title: Solution structure and NH exchange studies of the MutT pyrophosphohydrolase complexed with Mg(2+) and 8-oxo-dGMP, a tightly bound product. Authors: Massiah, M.A. / Saraswat, V. / Azurmendi, H.F. / Mildvan, A.S. #1: ![]() Title: Solution Structure of the Quaternary Complex MutT-M(2+)-AMPCPP-M(2+) Complex and Mechanism of its Pyrophosphohydrolase Action Authors: Lin, J. / Abeygunawardana, C. / Frick, D.N. / J Bessman, M. / Mildvan, A.S. #2: ![]() Title: NMR Studies of the Conformations and Location of Nucleotides Bound to the E.Coli MutT Enzyme Authors: Frick, D.N. / Weber, D.J. / Abeygunawardana, C. / Gittis, A.G. / J Bessman, M. / Mildvan, A.S. #3: ![]() Title: Solution Structure of the MutT Enzyme, a Nucleoside Triphosphate Pyrophosphohydrolase Authors: Abeygunawardana, C. / Weber, D.J. / Gittis, A.G. / Frick, D.N. / Lin, J. / Miller, A.F. / Bessman, M.J. / Mildvan, A.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 841.6 KB | Display | ![]() |
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PDB format | ![]() | 690.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 442.5 KB | Display | ![]() |
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Full document | ![]() | 637.7 KB | Display | |
Data in XML | ![]() | 97.5 KB | Display | |
Data in CIF | ![]() | 113.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 14945.029 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P08337, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-8OG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 1MM MUTT, 1.3MM 8-OXO-DGMP, 15MM MGCL2, 4MM D11-TRIS-HCL, PH 7.5, 21MM NACL, 0.34MM NAN3. Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 21 mM NaCl / pH: 7.5 / Pressure: ambient / Temperature: 295 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing torsion angle dynamics / Software ordinal: 1 Details: the structures are based on 1746 NOE-derived distance constraints, 186 dihedral angle restraints derived from TALOS, 82 distance restraints from hydrogen bonds and 3 assumed distances ...Details: the structures are based on 1746 NOE-derived distance constraints, 186 dihedral angle restraints derived from TALOS, 82 distance restraints from hydrogen bonds and 3 assumed distances ligand/protein (see Case 3, Table 1 in reference). | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 50 / Conformers submitted total number: 20 |